RetrogeneDB ID: retro_etel_173

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_2980:149300..149730(+)
• Located in intron of: ENSETEG00000015116

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: TMEM106C
• Ensembl ID: ENSETEG00000010370
• Aliases: None
• Description: transmembrane protein 106C [Source:HGNC Symbol;Acc:28775]

Sequence

>retro_etel_173
CCCTTCGTGGAGTTCACCCGGCAAAATAGCCTCACCTGCCTCCTGTGCCAAGGGACTGGCTACATCCCAACAGAACAAGT
CAAGAAGCTGGTGACTTAATTCCACACAGGAATCAGAGATCGTGTGCTCTGAGAACTCAACAGCATGGCCTGTCGATCTT
GCTCTGTCTGCTGGCCTCAGGGTTGCCCGTTTTCTTCCTGTTTCCCCTTTCAGTCCTTGTGGGTGAGGATGGCATCAAAG
TGGTGACAGTCTTAATAAAAAGGACTCCCTTGTCATGCTCGCCATCACAGCCACTTTGAAAATCAGCAACTCCAACTTCT
ACTCCGTGGCTGTAACCAGCCTGCCCAGCCAAGTTCAGTCCATGACCACAATGGTTAGTACCTACAAGACAACTGATGTC
ATCCTCATTCCGCCTTGCACCGAGCCACTG

Alignment

ORF - retro_etel_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.57 %
• Parental protein coverage: 58.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PYVEFTGRDSITCLTCQGTGYIPTEQVNELVA-LIPHSDQRLRPQRTKQYVLLSISLCLLVSGLVVFFLF
          P.VEFT...S.TCL.CQGTGYIPTEQV..LV..LIPH..QR....RT.Q...LSI.LCLL.SGL.VFFLF
Retrocopy PFVEFTRQNSLTCLLCQGTGYIPTEQVKKLVT<LIPHRNQRSCALRTQQHG-LSILLCLLASGLPVFFLF

Parental  PHSVLVDDDGIKVVKVLF-NKEESLVLLAITATLKIRNSNFYSVAVTSLSSQVQYMNTVVGTYGTTNVSL
          P.SVLV..DGIKVV.VL...K.....L.AITATLKI.NSNFYSVAVTSL.SQVQ.M.T.V.TY.TT.V.L
Retrocopy PLSVLVGEDGIKVVTVLI<KKDSLVML-AITATLKISNSNFYSVAVTSLPSQVQSMTTMVSTYKTTDVIL

Parental  IPPRSEQL
          IPP..E.L
Retrocopy IPPCTEPL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_173 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008335	1 retrocopy	retro_cpor_1124,
Equus caballus	ENSECAG00000020351	1 retrocopy	retro_ecab_660,
Echinops telfairi	ENSETEG00000010370	1 retrocopy	retro_etel_173 ,
Myotis lucifugus	ENSMLUG00000017734	1 retrocopy	retro_mluc_1096,
Pteropus vampyrus	ENSPVAG00000014352	1 retrocopy	retro_pvam_562,
Sus scrofa	ENSSSCG00000028397	1 retrocopy	retro_sscr_473,
Tarsius syrichta	ENSTSYG00000001184	1 retrocopy	retro_tsyr_1263,